Contacts of the helix formed by residues 73 - 81 (chain A) in PDB entry 3JRC
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 73 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A MET* 4.4 0.4 - - - -
70A THR* 3.0 30.1 + - - +
71A ARG* 3.2 2.1 + - + -
72A GLY* 1.3 73.9 - - - +
74A GLN* 1.3 62.1 + - - +
75A THR* 3.3 20.3 + - - -
76A ARG* 3.4 21.4 + - + +
77A ALA* 3.1 18.2 + - - +
5D T 3.0 39.6 + - - +
6D T 3.5 4.0 - - - -
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Residues in contact with GLN 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A MET* 3.2 25.9 - - + +
72A GLY 3.0 10.4 + - - +
73A ASN* 1.3 70.8 - - - +
75A THR* 1.3 63.1 + - - +
77A ALA* 4.6 0.2 - - - -
78A ALA* 3.1 22.0 + - - +
85A ARG* 4.7 8.6 - - + +
88A LEU* 3.3 17.7 - - + +
89A ARG* 3.4 42.1 + - - +
92A LEU* 3.4 28.2 - - + +
98A ASN* 5.6 6.9 - - - +
6D T 3.1 18.8 + - - +
7D G 4.4 10.1 + - - -
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Residues in contact with THR 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ASN* 3.2 10.0 - - - -
74A GLN* 1.3 77.3 - - - +
76A ARG* 1.3 66.7 + - + +
78A ALA* 3.5 2.2 + - - +
79A LEU* 3.1 40.4 + - + +
85A ARG* 3.8 14.8 - - - +
5D T 3.1 37.7 - - - +
6D T 2.9 34.9 + - + +
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Residues in contact with ARG 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A TYR* 5.3 8.1 - - - -
70A THR* 4.2 20.3 - - + +
73A ASN* 3.3 33.2 + - + +
75A THR* 1.3 79.1 - - + +
77A ALA* 1.3 53.6 + - - +
79A LEU* 3.1 14.0 + - + +
80A MET* 2.8 43.8 + - - +
5D T 3.6 11.0 - - - +
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Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL* 4.0 20.4 - - + -
67A MET* 4.5 7.0 - - - -
70A THR* 3.5 32.2 - - + +
73A ASN 3.1 10.3 + - - +
74A GLN 4.0 3.8 - - - +
76A ARG* 1.3 76.0 - - - +
78A ALA* 1.3 57.7 + - - +
80A MET* 3.5 5.0 - - - +
81A MET* 2.9 34.8 + - - +
88A LEU* 4.3 10.5 - - + -
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Residues in contact with ALA 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A GLN 3.1 17.9 + - - +
75A THR 3.7 5.2 - - - +
77A ALA* 1.3 76.7 - - - +
79A LEU* 1.3 62.0 + - + +
81A MET* 2.9 21.0 - - - +
82A GLY 4.1 0.3 - - - -
83A ILE* 2.9 36.7 + - - +
84A ASN 4.2 0.9 - - - -
85A ARG* 3.8 22.2 - - + +
88A LEU* 3.7 16.0 - - + +
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A THR* 3.1 31.0 - - + +
76A ARG* 3.1 14.0 + - + +
78A ALA* 1.3 78.3 - - + +
80A MET* 1.3 59.9 + - - +
81A MET 2.8 12.2 - - - +
83A ILE 5.0 1.8 - - - +
85A ARG* 6.2 1.8 - - + +
47B VAL 3.7 9.0 - - - +
48B ASN* 3.8 9.0 - - - +
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Residues in contact with MET 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL* 5.1 6.7 - - + -
69A TYR* 3.4 40.8 - - + -
70A THR* 4.2 11.2 - - - -
76A ARG* 2.8 23.2 + - - +
77A ALA* 3.5 7.6 - - - +
78A ALA 3.3 0.2 - - - -
79A LEU* 1.3 73.8 - - - +
81A MET* 1.3 64.2 + - + +
39B PHE* 3.4 28.9 - - + -
42B LEU* 4.4 3.1 - - + -
47B VAL* 3.6 40.2 - - + +
49B ASP 3.4 7.8 + - - -
50B LEU* 3.4 27.6 + - + +
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Residues in contact with MET 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU* 4.0 13.9 - - + -
63A LEU* 4.2 19.7 - - + -
66A VAL* 3.7 32.1 - - + -
77A ALA* 2.9 22.5 + - - +
78A ALA* 2.9 10.0 - - - +
79A LEU* 2.8 19.1 - - - +
80A MET* 1.3 76.2 - - - +
82A GLY* 1.3 59.5 + - - +
83A ILE* 3.3 28.9 - - + +
88A LEU* 5.3 2.5 - - - -
91A LYS* 6.4 0.2 - - + -
48B ASN 4.1 2.6 - - - +
49B ASP 4.4 0.9 - - - -
50B LEU* 3.8 23.1 - - + +
51B TYR* 3.6 35.9 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il